what version of gc2 are you using if its TA than nothing hardcoded it might be something as simple as deleting < this so check your spelling.

There are PLENTY of things that are still hardcoded, even in TA-and this is one of them.

1. The ability to speak to other civs is hardcoded into the UT tech, yes.  Sorry.  But you can of course change the display name, and in TA, you can even change the display name for each different race's tree.
2. It shouldn't be doing this; are you sure you've removed what you don't want from your own PI XML file?  It's supposed to replace (on an individual file basis), not extend, at least IIRC.  Are you running it out of its own mod folder that you have the game set to?
3. Sure, go into the ship component xml file and give them all tech requirements.  There are multiples of each, though, so you'll need to do them all.  As an aside, TA does this with one or two tinies and perhaps a cargo-and I didn't see the point, personally, with only doing it for some hulls of a type instead of all of them.
4. Only with custom maps/scenarios, and I don't remember specifically how.  But not in a normal sandbox pseudo-random map.  You might try altering the stats/functions on the default ships that you start with, but I'm not sure if that will accomplish what you're looking for.
5. I could have sworn there was an option for no anomalies.  There is not, however, any option with regards to either bonus tiles or resource crystals-although it has been discussed as a potentially beneficial setting a number of times.